Analysis of genetic effects on disease conferred by clusters of related and highly polymorphic genes poses substantial problems in terms of the identification of the true disease locus once an association has been observed. Understanding and accounting for the molecular genetic properties that operate over the locus is essential for accurate interpretation of both disease association data and analysis of functional interactions between the molecules encoded in the Major Histocompatibility Complex (MHC). Completion of the entire sequencing of the MHC has provided us with an invaluable tool for defining some of these properties. Comparing patterns of Linkage Disequilibrium (LD) between pairs of markers with recombination fractions for the segment separating those pairs of loci can provide information regarding selective pressure to maintain linkage of specific combinations of alleles. Measurements of LD between pairs of HLA class I and II genes, particularly in the Centre d'Etude Polymorphisme Humain (CEPH) families, have emerged over the past several years, revealing significant associations between loci separated by distances of >1 Mb. Previous studies of recombination using segregation analysis have suggested that overall, recombination across the MHC is lower than expected, although the use of family material for the generation of such information is severely limited in power. Detailed mapping of recombination using sperm typing has been performed within a 200 kb segment of the class II locus in the region of the genes DNA and DMB, showing a strong correlation between recombination fraction and LD values for pairs of markers over this short segment. In order to generate a reliable estimate of the frequency and distribution of recombination events across the entire MHC, we used single-sperm typing of microsatellite markers previously identified by us. Genotyping of 20,031 single sperm from 12 individuals resulted in the identification and fine mapping of 325 recombinant chromosomes. In this study, we found that recombination rate in hot spots may vary between individuals. For example, a region in HLA class III located between the BAT2 and LTA genes (45 kb), which was characterized as the strongest hot spot within the MHC, actually exhibited significant variation in recombination rate across individual sperm donors. We hypothesized that level of the sequence similarity between homologous chromosomes of a given individual in a particular chromosomal segment and rate of recombination would be correlated positively. Thus, we have begun to sequence this 45 kb fragment in 6 individuals whose recombination rates vary significantly in this area. The region is being amplified in 10 overlapping 5-6 kb segments and the Sanger Centre (Cambridge, UK) has agreed to make mini-libraries of each 5-6Kb amplicon and sequence multiple clones, creating contigs. Complete sequences of the 45 kb fragment will be assembled by our laboratory, and the level of sequence similarity will be analyzed in each individual to determine if there is a correlation with recombination rate. Through the International Histocompatibility Workshops, HLA allelic distributions across populations have been investigated. This organized transcontinental cooperation among HLA typing labs provides a unique and invaluable resource of HLA data that may not otherwise be available to the community. Historically, however, the data have suffered limitations in terms of typing resolution, consistency in typing protocols across laboratories, and numbers of samples typed for some populations. We have had the fortunate opportunity to genotype both the HLA class I and killer immunoglobulin receptors (KIR) loci in sets of samples (ranging in size from 23-129 individuals) from 29 worldwide populations. KIR and HLA typing have been completed on the majority of the 1612 samples sent to us and we will soon begin the process of analyzing the data. We have also received 320 DNA samples representing distinct tribes from rural southern Cameroon that will be included in our population analysis of these genes. Consideration of these data in terms of the geographic origins of the various populations may provide clues to potential selection processes that have occurred differentially across the populations.